http://stackoverflow.com/questions/21515463/how-to-increase-maximum-file-open-limit-ulimit-in-ubuntu

gistfile1.txt

the ulimit command by default changes the HARD limits, which you (a user) can lower, but cannot raise.

Use the -S option to change the SOFT limit, which can range from 0-{HARD}.

I have actually aliased 'ulimit' to 'ulimit -S', so it defaults to the soft limits all the time.

alias ulimit='ulimit -S'
As for your issue, you're missing a column in your entries in limits.conf

There should be FOUR colums, the first is missing in your example.

* soft nofile 4096
* hard nofile 4096
The first column describes WHO the limit is to apply for. '*' is a wildcard, meaning all users. To raise the limits for root, you have to explicitly enter 'root' instead of '*'.

You also need to edit /etc/pam.d/common-session* and add the following line to the end:

session required pam_limits.so